Noncoding RNAs are genes for which RNA, rather than protein, is the functional end product. These noncoding genes come in many types. RNAs which have structural or catalytic roles in larger complexes are well known, such as ribosomal RNAs and transfer RNAs. However, the number and diversity of other noncoding RNAs in bacteria remain poorly understood. The majority of small, noncoding RNAs in bacteria appear to act as post-transcriptional regulators by basepairing with target messenger RNAs. Only a handful of these RNA genes have been identified, although it is estimated that they compose between 1% and 5% of bacterial genes. This project seeks to elucidate the functional roles of noncoding RNA genes in bacteria through bioinformatics methods. Two specific aims will be pursued: 1) A probabilistic model will be developed for characterizing small, noncoding RNAs in bacterial genomes. The model will incorporate three heterogeneous sources of data (primary sequence data, conserved RNA structure information from comparative genomics analyses, and microarray expression data) for the purpose of predicting previously uncharacterized noncoding RNAs in bacteria. 2) A model will be developed for characterizing the interactions between small, noncoding RNAs in bacteria and their message targets. The model will be used to predict novel messenger RNA targets of small, noncoding RNA regulation. While the bioinformatics approaches developed in this project will be applicable to prokaryotes more broadly, the approaches will be validated experimentally in Escherichia coli and Pseudomonas aeruginosa. [unreadable] [unreadable] [unreadable]